Deposition

Agent-Curated Membrane Segmentations and Compartment Annotations for Bdellovibrio bacteriovorus Cryo-ET Data.

Deposition ID:CZCDP-10338

Release Date: 2026-04-20

Last Modified: 2026-04-20

key visualization for Agent-Curated Membrane Segmentations and Compartment Annotations for Bdellovibrio bacteriovorus Cryo-ET Data.

Photo Caption: Central slab of 4 representative tomograms with selected sets of annotations.

Deposition Overview

Agent-curated membrane segmentations and compartment annotations (cell, cytoplasm, periplasmic space, and bacterial-type flagellum) for Bdellovibrio bacteriovorus cryo-ET data. Segmentations were produced by combining automated membrane predictions with semi-manual annotations created using napari-nnInteractive, followed by an agent-designed curation pipeline generated through copick-mcp.

Authors

Deposition Data

Annotations:82

Tomograms:0

Publications

DOI:10.1002/pro.70578

Related Databases

Not Submitted

Methods Summary

Annotations	Method Type	Method Details	Method Links
36	Hybrid	curation using copick-mcp and copick-utils	Source Code:copick-mcp +1 more
10	Hybrid	membrain-seg prediction, curation using copick-mcp and copick-utils	Source Code:copick-mcp +1 more
36	Hybrid	semi-manual annotation using napari-nnInteractive	Source Code:Napari-nnInteractive

Deposited Data

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Data Contents

Tilt SeriesAvailable

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82 of 82 Annotations

Annotation Name	Object Shape Type	Method Type	Deposited In
110membrane Annotation ID: AN-141365	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-43
109periplasmic space Annotation ID: AN-141364	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-43
108dense body Annotation ID: AN-141363	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-43
107bacterial-type flagellum Annotation ID: AN-141362	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-43
106cytoplasm Annotation ID: AN-141361	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-43
105dense body Annotation ID: AN-141360	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-43
104bacterial-type flagellum Annotation ID: AN-141359	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-43
103cytoplasm Annotation ID: AN-141358	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-43
102cell Annotation ID: AN-141357	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-43
109membrane Annotation ID: AN-141356	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-39
108periplasmic space Annotation ID: AN-141355	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-39
107bacterial-type flagellum Annotation ID: AN-141354	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-39
106cytoplasm Annotation ID: AN-141353	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-39
105bacterial-type flagellum Annotation ID: AN-141352	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-39
104cytoplasm Annotation ID: AN-141351	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-39
103cell Annotation ID: AN-141350	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-39
109membrane Annotation ID: AN-141349	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-36
108periplasmic space Annotation ID: AN-141348	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-36
107dense body Annotation ID: AN-141347	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-36
106cytoplasm Annotation ID: AN-141346	SegmentationMask	Hybrid	Dataset: Bdellovibrio attack-phase Run: ycw2013-09-10-36